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Site-specific dN/dS values across the ZIKV polyprotein. (a) Zika virus site-specific dN/dS analysis measured using 517 Zika virus isolates. Box plots: posterior probability distributions of dN/dS values across the Zika virus genome. Red bars: clade-defining loci. (b) Posterior probability densities for the five clade-defining amino acid loci that have dN/dS values greater than one. (c) The number of synonymous, nonsynonymous, and clade-defining mutations across the Zika virus genome. Clade-specific amino acid sites have significantly higher dN/dS values (p = .0002; Mann-Whitney U test) when compared to the remaining amino acid sites with nonsynonymous mutations. https://doi.org/10.1371/journal.pntd.0011055.g005
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RNA viruses have short generation times and high mutation rates, allowing them to undergo rapid molecular evolution during epidemics. However, the extent of RNA virus phenotypic evolution within epidemics and the resulting effects on fitness and virulence remain mostly unknown. Here, we screened the 2015-2016 Zika epidemic in the Americas for linea...
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Context 1
... we applied renaissance counting [30] selection analysis to our 517 sequences to calculate site-specific dN/dS values across the protein-coding region of the Zika virus genome. Among the ~3,420 amino acid sites in the Zika virus genome, we identified 25 sites that had 90% of their posterior dN/dS distributions greater than one (Fig 5A and 5B). Five of 17 lineage-defining mutations were among the 25 putative sites under positive selection (clades B; NS1-M349V, C; NS5-I322V, G; NS5-T833A, H; C-I80T, and PA2; NS3-Y584H), with average posterior dN/dS ratios ranging from 1.2-1.9 ...
Context 2
... of 17 lineage-defining mutations were among the 25 putative sites under positive selection (clades B; NS1-M349V, C; NS5-I322V, G; NS5-T833A, H; C-I80T, and PA2; NS3-Y584H), with average posterior dN/dS ratios ranging from 1.2-1.9 (Fig 5A and 5B). Throughout the Zika virus genome, 20 amino acid sites that did not define major clades had dN/dS values greater than one, and two of these sites were within two codons from a clade-defining mutation (clades E and PA2). ...
Context 3
... average dN/dS values for synonymous only, nonsynonymous, and cladedefining sites were 0.07, 0.53, and 0.76, respectively. Next, we compared the clade-defining amino acid sites with all other nonsynonymous, amino acid-specific dN/dS values, and we found that the clade-defining values were significantly higher (Mann-Whitney U test, p = 0.04; Fig 5D and 5E). This shows that lineage-defining amino acid sites tend to have higher dN/dS ratios than non-lineage-defining sites, suggesting that our sites are either under increased positive selection or relaxed purifying selection. ...
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Dengue fever is a dengue virus infection, emerging rapidly and posing public health threat worldwide, primarily in tropical and subtropical countries. Nearly half of the world's population is now at risk of contracting the dengue virus, including new countries with no previous history-like Ethiopia. However, little is known about the epidemiology a...
Citations
... Finally, considerable research effort has been dedicated to identifying mutations that may have contributed to Zika virus (ZIKV) epidemic potential or contributed to the appearance of previously unobserved severe clinical manifestations [reviewed in reference (9)]. Whether these mutations are important determinants of ZIKV emergence and spread remains an open question (10)(11)(12). ...
Zika virus (ZIKV) is now in a post-pandemic period, for which the potential for re-emergence and future spread is unknown. Adding to this uncertainty is the unique capacity of ZIKV to directly transmit between humans via sexual transmission. Recently, we demonstrated that direct transmission of ZIKV between vertebrate hosts leads to rapid adaptation resulting in enhanced virulence in mice and the emergence of three amino acid substitutions (NS2A-A117V, NS2A-A117T, and NS4A-E19G) shared among all vertebrate-passaged lineages. Here, we further characterized these host-adapted viruses and found that vertebrate-passaged viruses do not lose fitness or transmission potential in mosquitoes. To understand the contribution of genetic changes to the enhanced virulence and transmission phenotype, we engineered these amino acid substitutions, singly and in combination, into a ZIKV infectious clone. We found that NS4A-E19G contributed to the enhanced virulence and mortality phenotype in mice. Further analyses revealed that NS4A-E19G results in increased viral loads and distinct transcriptional patterns for innate immune genes in the brain. None of the substitutions contributed to changes in mosquito vector competence. Together, these findings suggest that direct transmission chains could enable the emergence of more virulent ZIKV strains without compromising mosquito transmission capacity, although the underlying genetics of these adaptations are complex.
IMPORTANCE
Previously, we modeled direct transmission chains of Zika virus (ZIKV) by serially passaging ZIKV in mice and mosquitoes and found that direct mouse transmission chains selected for viruses with increased virulence in mice and the acquisition of non-synonymous amino acid substitutions. Here, we show that these same mouse-passaged viruses also maintain fitness and transmission capacity in mosquitoes. We used infectious clone-derived viruses to demonstrate that the substitution in nonstructural protein 4A contributes to increased virulence in mice.
Zika virus (ZIKV) is now in a post-pandemic period, for which the potential for re-emergence and future spread is unknown. Adding to this uncertainty is the unique capacity of ZIKV to directly transmit between humans via sexual transmission. Recently, we demonstrated that direct transmission of ZIKV between vertebrate hosts leads to rapid adaptation resulting in enhanced virulence in mice and the emergence of three amino acid substitutions (NS2A-A117V, NS2A-A117T, and NS4A-E19G) shared among all vertebrate-passaged lineages. Here, we further characterized these host-adapted viruses and found that vertebrate-passaged viruses also have enhanced transmission potential in mosquitoes. To understand the contribution of genetic changes to the enhanced virulence and transmission phenotype, we engineered these amino acid substitutions, singly and in combination, into a ZIKV infectious clone. We found that NS4A-E19G contributed to the enhanced virulence and mortality phenotype in mice. Further analyses revealed that NS4A-E19G results in increased neurotropism and distinct innate immune signaling patterns in the brain. None of the substitutions contributed to changes in transmission potential in mosquitoes. Together, these findings suggest that direct transmission chains could enable the emergence of more virulent ZIKV strains without compromising mosquito transmission capacity, although the underlying genetics of these adaptations are complex.
